Searches for the matrix with the higher probability of having a CGCGCG primer (only one solution). Minimizes 1-p(CGCGCG)
test.perf <- read.csv('~/mnt/edann/hexamers/strand_specific/test_function.performance.csv', header = FALSE, col.names = c('it','score'))
head(test.perf)
Functions for reshaping and plotting are in DE_performance.r
max(long.mat$iter)
[1] "999"
l <- lapply(seq(1,3), function(i) plot.iteration(long.mat, i))
# png('~/AvOwork/output/DE_optimization/test_iter_matrix.png')
for(el in l){
# png(paste0("~/AvOwork/output/DE_optimization/DE_iter-", el$data$iter[1], ".png"))
plot(el)
# dev.off()
}
With bigger population size I get better scores and if the algorithm gets stuck in a local minimum it happens after more iterations.
rho.files.10 <- list.files(opt.dir, pattern='_pop10_its300.DE.rho.txt', full.names = TRUE)
rho.files.20 <- list.files(opt.dir, pattern='_pop20_its300.DE.rho.txt', full.names = TRUE)
rho.files.30 <- list.files(opt.dir, pattern='_pop30_its300.DE.rho.txt', full.names = TRUE)
plot.optimization.score(rho.files.10) +
ggtitle('Pop.size=10')
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plot.optimization.score(rho.files.20) +
ggtitle('Pop.size=20')
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plot.optimization.score(rho.files.30) +
ggtitle('Pop.size=30')
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plot.optimization.score(score.ctcf.files)
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performance.mat <- read.csv(matrix.ctcf.files[4], row.names = 1)
long.mat <- reshape.prob.mat(performance.mat)
Using iter as id variables
head(performance.mat)
nrow(performance.mat)
[1] 100
lapply(matrix.ctcf.files, function(mat)
plot.iteration(reshape.prob.mat(read.csv(mat, row.names = 1)),99) +
ggtitle(gsub(mat, pattern = '.+//', replacement = '')))
Using iter as id variables
Using iter as id variables
Using iter as id variables
Using iter as id variables
Using iter as id variables
Using iter as id variables
Using iter as id variables
Using iter as id variables
Using iter as id variables
Using iter as id variables
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]
[[10]]
Test4 is so weird! Best score and ends with all Ts!!
performance.mat <- read.csv(matrix.ctcf.files[5], row.names = 1)
long.mat <- reshape.prob.mat(performance.mat)
lapply(c(1,10,20,50,70,99),function(it) plot.iteration(long.mat, it))
bestmat.bw <- import(bestmat.bw.file, format = 'BigWig')
Error in import(bestmat.bw.file, format = "BigWig") :
could not find function "import"
plot.refpoint.profile.df(not.norm.bestmat.df)
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plot.refpoint.profile.df(norm.bestmat.df)
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Not total abundance
plot.optimization.score(score.ctcf.files) +
theme(legend.title = element_blank())
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plot.optimization.score(score.ctcf.files) +
theme(legend.title = element_blank())
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plot.optimization.score(score.ctcf.files) +
theme(legend.title = element_blank())
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Load coverage profiles around CTCF sites
prof.files <- list.files(paste0(opt.dir,'predicted_cov_bestmat'), pattern = 'profile.txt', full.names = T)
profiles <- lapply(prof.files, load.profile)
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names(profiles) <- gsub(prof.files, pattern = '.+500reg|.bestMat.+profile.txt', replacement = '')
df <- make.df.of.profiles(profiles)
best.scores <- sapply(score.ctcf.files, function(x) rev.default(scan(x))[1])
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names(best.scores) <- gsub(names(best.scores), pattern = '.+/|.DE.+.txt', replacement = '')
df.wScores <- df %>% mutate(score=best.scores[match(df$sample, names(best.scores))])
df.wScores %>%
filter(sample!='test1_ctcf_kmersFC_pop30_its100') %>%
filter(sample!="test10_ctcf_kmersFC_pop30_its100") %>%
plot.refpoint.profile.df(., color = 'score') +
guides(color = guide_colorbar(barwidth = 20, barheight = 1))
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Not normalized
profiles <- lapply(prof.files, load.profile, normalize=F)
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names(profiles) <- gsub(prof.files, pattern = '.+500reg|.bestMat.+profile.txt', replacement = '')
df <- make.df.of.profiles(profiles)
best.scores <- sapply(score.ctcf.files, function(x) rev.default(scan(x))[1])
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names(best.scores) <- gsub(names(best.scores), pattern = '.+/|.DE.+.txt', replacement = '')
df.wScores <- df %>% mutate(score=best.scores[match(df$sample, names(best.scores))])
df.wScores %>%
filter(sample!='test1_ctcf_kmersFC_pop30_its100') %>%
filter(sample!="test10_ctcf_kmersFC_pop30_its100") %>%
plot.refpoint.profile.df(., color = 'score') +
guides(color = guide_colorbar(barwidth = 20, barheight = 1))
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plot.expVSpred.coverage.track(l.best.bw[[2]])
The following non-numeric data column has been dropped: id
[[1]]
Genome axis 'Axis'
[[2]]
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr1
| positions: 4999
| samples:1
| strand: *
regionsWctcf
[1] "chr1 (1.82535e+08,1.8269e+08]" "chr10 (8.91e+06,9.78e+06]" "chr11 (7.0175e+07,7.032e+07]" "chr13 (5.801e+07,5.816e+07]"
[5] "chr13 (9.9375e+07,9.9725e+07]" "chr14 (2.1045e+07,2.111e+07]" "chr14 (6.985e+07,6.989e+07]" "chr15 (5.847e+07,5.878e+07]"
[9] "chr17 (2.6425e+07,2.6595e+07]" "chr17 (2.776e+07,2.8335e+07]" "chr17 (2.776e+07,2.8335e+07]" "chr18 (6.0855e+07,6.1005e+07]"
[13] "chr18 (6.4525e+07,6.461e+07]" "chr18 (6.727e+07,6.7355e+07]" "chr19 (3.2715e+07,3.305e+07]" "chr19 (4.366e+07,4.4e+07]"
[17] "chr2 (1.2636e+08,1.26775e+08]" "chr2 (1.5342e+08,1.53505e+08]" "chr4 (9.78e+06,9.88e+06]" "chr6 (3.416e+07,3.426e+07]"
[21] "chr6 (8.3135e+07,8.323e+07]" "chr6 (1.48705e+08,1.49265e+08]" "chr7 (2.524e+07,2.552e+07]" "chr7 (2.8335e+07,2.946e+07]"
[25] "chr7 (2.8335e+07,2.946e+07]" "chr7 (9.7675e+07,9.8015e+07]" "chr7 (1.4244e+08,1.4268e+08]" "chr8 (2.4525e+07,2.481e+07]"
[29] "chr8 (5.366e+07,5.367e+07]" "chr8 (8.4695e+07,8.47e+07]" "chr8 (8.4695e+07,8.47e+07]" "chr8 (1.0857e+08,1.08725e+08]"
[33] "chr9 (1.06345e+08,1.06605e+08]" "chrX (1.53505e+08,1.5367e+08]"
lapply(sample(regionsWctcf,10), function(x) plot.cov.wAnnotation(l.best.bw[x][[1]], ctcf))
The following non-numeric data column has been dropped: id
[[1]]
[[1]]$Axis
Genome axis 'Axis'
[[1]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr1
| positions: 5000
| samples:1
| strand: *
[[1]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr1
| annotation features: 1
[[1]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
[[2]]
[[2]]$Axis
Genome axis 'Axis'
[[2]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr19
| positions: 4999
| samples:1
| strand: *
[[2]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr19
| annotation features: 1
[[2]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
[[3]]
[[3]]$Axis
Genome axis 'Axis'
[[3]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr7
| positions: 4999
| samples:1
| strand: *
[[3]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr7
| annotation features: 2
[[3]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
[[4]]
[[4]]$Axis
Genome axis 'Axis'
[[4]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr14
| positions: 4999
| samples:1
| strand: *
[[4]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr14
| annotation features: 1
[[4]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
[[5]]
[[5]]$Axis
Genome axis 'Axis'
[[5]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr17
| positions: 4999
| samples:1
| strand: *
[[5]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr17
| annotation features: 2
[[5]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
[[6]]
[[6]]$Axis
Genome axis 'Axis'
[[6]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr8
| positions: 4999
| samples:1
| strand: *
[[6]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr8
| annotation features: 2
[[6]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
[[7]]
[[7]]$Axis
Genome axis 'Axis'
[[7]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr13
| positions: 4999
| samples:1
| strand: *
[[7]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr13
| annotation features: 1
[[7]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
[[8]]
[[8]]$Axis
Genome axis 'Axis'
[[8]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr18
| positions: 4999
| samples:1
| strand: *
[[8]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr18
| annotation features: 1
[[8]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
[[9]]
[[9]]$Axis
Genome axis 'Axis'
[[9]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr17
| positions: 4999
| samples:1
| strand: *
[[9]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr17
| annotation features: 2
[[9]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
[[10]]
[[10]]$Axis
Genome axis 'Axis'
[[10]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr8
| positions: 4999
| samples:1
| strand: *
[[10]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr8
| annotation features: 2
[[10]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
Compare with even primer probability predicted coverage
plot.expVSpred.coverage.track(l.comon.bw[[2]])
The following non-numeric data column has been dropped: id
[[1]]
Genome axis 'Axis'
[[2]]
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr1
| positions: 4999
| samples:2
| strand: *
lapply(sample(regionsWctcf,10), function(x) plot.cov.wAnnotation(l.comon.bw[x][[1]], ctcf))
The following non-numeric data column has been dropped: id
[[1]]
[[1]]$Axis
Genome axis 'Axis'
[[1]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr8
| positions: 4999
| samples:2
| strand: *
[[1]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr8
| annotation features: 1
[[1]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
[[2]]
[[2]]$Axis
Genome axis 'Axis'
[[2]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr19
| positions: 4999
| samples:2
| strand: *
[[2]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr19
| annotation features: 1
[[2]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
[[3]]
[[3]]$Axis
Genome axis 'Axis'
[[3]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr7
| positions: 4999
| samples:2
| strand: *
[[3]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr7
| annotation features: 1
[[3]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
[[4]]
[[4]]$Axis
Genome axis 'Axis'
[[4]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr8
| positions: 4999
| samples:2
| strand: *
[[4]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr8
| annotation features: 1
[[4]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
[[5]]
[[5]]$Axis
Genome axis 'Axis'
[[5]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr7
| positions: 4999
| samples:2
| strand: *
[[5]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr7
| annotation features: 2
[[5]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
[[6]]
[[6]]$Axis
Genome axis 'Axis'
[[6]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr18
| positions: 4999
| samples:2
| strand: *
[[6]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr18
| annotation features: 1
[[6]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
[[7]]
[[7]]$Axis
Genome axis 'Axis'
[[7]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr6
| positions: 4999
| samples:2
| strand: *
[[7]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr6
| annotation features: 1
[[7]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
[[8]]
[[8]]$Axis
Genome axis 'Axis'
[[8]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr2
| positions: 5000
| samples:2
| strand: *
[[8]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr2
| annotation features: 1
[[8]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
[[9]]
[[9]]$Axis
Genome axis 'Axis'
[[9]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr4
| positions: 4999
| samples:2
| strand: *
[[9]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr4
| annotation features: 1
[[9]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
[[10]]
[[10]]$Axis
Genome axis 'Axis'
[[10]]$`norm. coverage`
DataTrack 'norm. coverage'
| genome: NA
| active chromosome: chr1
| positions: 5000
| samples:2
| strand: *
[[10]]$CTCF
AnnotationTrack 'CTCF'
| genome: NA
| active chromosome: chr1
| annotation features: 1
[[10]]$titles
An object of class "ImageMap"
Slot "coords":
x1 y1 x2 y2
Axis 6 37.24747 38.42335 77.20723
norm. coverage 6 77.20723 38.42335 278.26342
CTCF 6 278.26342 38.42335 318.47466
Slot "tags":
$title
Axis norm. coverage CTCF
"Axis" "norm. coverage" "CTCF"
plot.refpoint.profile.df(df)
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But here I am comparing noisy data (500 regions) and not noisy data (5000 regions)
plot.optimization.score(score.even.files) +
theme(legend.title = element_blank())
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Doesn’t seem to play a major role.
Visualizing in another way
Nope.